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Crystal Structure of Helicobacter pylori Urease Accessory Protein UreE(1-148) and UreG in complex with GMPPNP and nickel.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XKT experimental model PDB 3TJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 Crystal was obtained by mixing 2 ul protein sample (10mg/ml) with 1 ul 0.2M sodium malonate dibase monohydrate, 0.1M bis-tris propane, 18% PEG3350, 2 mM Nickel sulfate, 4 mM Magnesium sulfate, and 5mM GMPPNP at 289K.
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.97 α = 90 b = 151.067 β = 99.495 c = 83.147 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2019-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.85 42.91 99.6 0.995 8.4 3.6 40057 58.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.97 0.812
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5XKT,3TJ8 2.85 42.91 1.34 40057 1919 99.35 0.244 0.2426 0.2419 0.2719 0.2733 63.71
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.5718 f_angle_d 0.5694 f_chiral_restr 0.0466 f_plane_restr 0.0037 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10356 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 134
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing